Grouped analysis results

Parameters	Input values
Folder name :	Example data
Sequence name :	Test sequence
Reference genome :	BSgenome.Hsapiens.UCSC.hg19
Type of experiment :	Direct-BSP
Group order :	group1, group2
Date of analysis :	2022-06-04 18:35

Files content

Data files content

Parameters	Data files content
Sequence name :	Test sequence
Collections :	collection1, collection2
Groups :	group1, group2
Replicates :	1, 2, 3

Data files paths

File paths used for the analysis

D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_direct/data/Test sequence_collection1_group1_1_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_direct/data/Test sequence_collection1_group1_2_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_direct/data/Test sequence_collection1_group1_3_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_direct/data/Test sequence_collection1_group2_1_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_direct/data/Test sequence_collection1_group2_2_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_direct/data/Test sequence_collection1_group2_3_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_direct/data/Test sequence_collection2_group1_1_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_direct/data/Test sequence_collection2_group1_2_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_direct/data/Test sequence_collection2_group1_3_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_direct/data/Test sequence_collection2_group2_1_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_direct/data/Test sequence_collection2_group2_2_methdata.csv
D:/Documents/These/ABSP/results/Example data/Test sequence/individual_results_direct/data/Test sequence_collection2_group2_3_methdata.csv

Methylation data

Methylation data of replicates

	chr16:68770595-68770596	chr16:68770613-68770614	chr16:68770646-68770647	chr16:68770665-68770666	chr16:68770670-68770671	chr16:68770717-68770718	Mean	SD
collection1 group1 1	38.44	21.17	5.56	24.31	0.00	12.61	17.02	13.93
collection1 group1 2	18.65	12.84	16.93	19.07	0.00	20.09	14.60	7.59
collection1 group1 3	6.12	8.25	24.85	6.69	32.95	16.63	15.92	11.05
collection1 group2 1	67.41	83.83	84.18	85.67	100.00	74.04	82.52	11.14
collection1 group2 2	55.41	75.91	60.26	52.01	100.00	67.33	68.49	17.66
collection1 group2 3	98.62	65.18	56.78	82.81	70.73	90.10	77.37	15.87
collection2 group1 1	21.60	13.38	24.98	31.74	4.84	20.58	19.52	9.36
collection2 group1 2	38.62	0.00	52.73	16.17	36.61	0.00	24.02	21.96
collection2 group1 3	19.37	3.66	43.99	4.87	33.12	25.27	21.71	15.84
collection2 group2 1	61.26	63.68	83.57	71.25	56.68	93.89	71.72	14.37
collection2 group2 2	62.96	91.07	86.62	61.63	78.68	80.02	76.83	12.13
collection2 group2 3	72.37	65.22	70.84	82.10	81.23	66.92	73.11	7.11

Methylation data of groups

	chr16:68770595-68770596	chr16:68770613-68770614	chr16:68770646-68770647	chr16:68770665-68770666	chr16:68770670-68770671	chr16:68770717-68770718	Mean	SD
collection1 group1	21.07	14.09	15.78	16.69	10.98	16.44	15.84	3.32
collection1 group2	73.81	74.97	67.07	73.50	90.24	77.16	76.12	7.69
collection2 group1	26.53	5.68	40.57	17.59	24.86	15.28	21.75	11.87
collection2 group2	65.53	73.32	80.34	71.66	72.20	80.28	73.89	5.67

Plots of replicates

Lollipop plots

Sample order : as-is

Type : proportional

Type : condensed

Sample order : by-group

Type : proportional

Type : condensed

Sample order : by-meth

Type : proportional

Type : condensed

Sample order : clust

Type : proportional

Type : condensed

Genomic plots

Sample order : as-is

Sample order : by-group

Sample order : by-meth

Sample order : clust

Plots of groups

Lollipop plots

Sample order : as-is

Type : proportional

Type : condensed

Sample order : by-group

Type : proportional

Type : condensed

Sample order : by-meth

Type : proportional

Type : condensed

Sample order : clust

Type : proportional

Type : condensed

Genomic plots

Sample order : as-is

Sample order : by-group

Sample order : by-meth

Sample order : clust

Statistics

Descriptive statistics of groups

Methylation by CpG positions

CpG number	CpG coordinate	Collection	Group	N	Methylation mean	SD	SEM	Confidence interval of 95% (±)
1	chr16:68770595-68770596	collection1	group1	3	21.07	16.30	9.41	40.48
1	chr16:68770595-68770596	collection1	group2	3	73.81	22.31	12.88	55.41
1	chr16:68770595-68770596	collection2	group1	3	26.53	10.53	6.08	26.16
1	chr16:68770595-68770596	collection2	group2	3	65.53	5.98	3.46	14.87
2	chr16:68770613-68770614	collection1	group1	3	14.09	6.55	3.78	16.27
2	chr16:68770613-68770614	collection1	group2	3	74.97	9.36	5.40	23.25
2	chr16:68770613-68770614	collection2	group1	3	5.68	6.91	3.99	17.18
2	chr16:68770613-68770614	collection2	group2	3	73.32	15.39	8.88	38.23
3	chr16:68770646-68770647	collection1	group1	3	15.78	9.70	5.60	24.09
3	chr16:68770646-68770647	collection1	group2	3	67.07	14.92	8.61	37.05
3	chr16:68770646-68770647	collection2	group1	3	40.57	14.19	8.19	35.25
3	chr16:68770646-68770647	collection2	group2	3	80.34	8.37	4.83	20.79
4	chr16:68770665-68770666	collection1	group1	3	16.69	9.05	5.22	22.48
4	chr16:68770665-68770666	collection1	group2	3	73.50	18.66	10.78	46.36
4	chr16:68770665-68770666	collection2	group1	3	17.59	13.49	7.79	33.51
4	chr16:68770665-68770666	collection2	group2	3	71.66	10.24	5.91	25.44
5	chr16:68770670-68770671	collection1	group1	3	10.98	19.02	10.98	47.26
5	chr16:68770670-68770671	collection1	group2	3	90.24	16.90	9.76	41.98
5	chr16:68770670-68770671	collection2	group1	3	24.86	17.42	10.06	43.28
5	chr16:68770670-68770671	collection2	group2	3	72.20	13.50	7.79	33.53
6	chr16:68770717-68770718	collection1	group1	3	16.44	3.74	2.16	9.30
6	chr16:68770717-68770718	collection1	group2	3	77.16	11.70	6.76	29.07
6	chr16:68770717-68770718	collection2	group1	3	15.28	13.44	7.76	33.39
6	chr16:68770717-68770718	collection2	group2	3	80.28	13.49	7.79	33.50

Methylation means of all CpG positions

Collection	Group	N	Methylation mean	SD	SEM	Confidence interval of 95% (±)
collection1	group1	3	15.85	1.21	0.70	3.01
collection1	group2	3	76.13	7.10	4.10	17.63
collection2	group1	3	21.75	2.25	1.30	5.59
collection2	group2	3	73.89	2.64	1.53	6.56

Student’s T test

For each CpG position

Student’s T test (two-samples, unpaired).

CpG number	CpG coordinate	Collection	Compared group 1	Compared group 2	N group 1	N group 2	p-value	p-value significance level
1	chr16:68770595-68770596	collection1	group1	group2	3	3	0.03390	*
2	chr16:68770613-68770614	collection1	group1	group2	3	3	0.00127	**
3	chr16:68770646-68770647	collection1	group1	group2	3	3	0.01110	*
4	chr16:68770665-68770666	collection1	group1	group2	3	3	0.01930	*
5	chr16:68770670-68770671	collection1	group1	group2	3	3	0.00594	**
6	chr16:68770717-68770718	collection1	group1	group2	3	3	0.00741	**
1	chr16:68770595-68770596	collection2	group1	group2	3	3	0.00981	**
2	chr16:68770613-68770614	collection2	group1	group2	3	3	0.00784	**
3	chr16:68770646-68770647	collection2	group1	group2	3	3	0.02140	*
4	chr16:68770665-68770666	collection2	group1	group2	3	3	0.00640	**
5	chr16:68770670-68770671	collection2	group1	group2	3	3	0.02280	*
6	chr16:68770717-68770718	collection2	group1	group2	3	3	0.00410	**

For means of CpG positions

Student’s T test (two-samples, unpaired).

Collection	Compared group 1	Compared group 2	N group 1	N group 2	p-value	p-value significance level
collection1	group1	group2	3	3	3.74e-03	**
collection2	group1	group2	3	3	1.61e-05	****

Boxplots

For each CpG position

Boxplots represent methylation median and quartiles of each group with errors bars. Methylation mean are represented as diamond shapes.

The p-values and p-value significance levels are determined by Student's T tests (two-samples, unpaired).

p-values

Open boxplot image in a new tab.

p-values significance levels

Open boxplot image in a new tab.

For means of CpG positions

Boxplots represent methylation median and quartiles of each group with errors bars. Methylation mean are represented as diamond shapes.

The p-values and p-value significance levels are determined by Student's T tests (two-samples, unpaired).

p-values

Open boxplot image in a new tab.

p-values significance levels

Open boxplot image in a new tab.

Methylation profile plots

Each points represent the methylation mean of clones or replicates for a given CpG site.
The p-values and p-value significance levels are determined by Kruskal-Wallis tests.

collection1

Type : proportional

p-values

p-values significance levels

Type : condensed

p-values

p-values significance levels

collection2

Type : proportional

p-values

p-values significance levels

Type : condensed

p-values

p-values significance levels

Output data

Directories

Files

boxplots

Test sequence_boxplot_means_psign.png

Test sequence_boxplot_means_pval.png

Test sequence_boxplot_positions_psign.png

Test sequence_boxplot_positions_pval.png

dendro_plots

Test sequence_dendro_groups.png

Test sequence_dendro_replicates.png

genomic_plots

legend_bases.png

Test sequence_genomic_groups_as-is.png

Test sequence_genomic_groups_by-group.png

Test sequence_genomic_groups_by-meth.png

Test sequence_genomic_groups_clust.png

Test sequence_genomic_replicates_as-is.png

Test sequence_genomic_replicates_by-group.png

Test sequence_genomic_replicates_by-meth.png

Test sequence_genomic_replicates_clust.png

lollipop_plots

Test sequence_lollipop_groups_as-is_condensed.png

Test sequence_lollipop_groups_as-is_proportional.png

Test sequence_lollipop_groups_by-group_condensed.png

Test sequence_lollipop_groups_by-group_proportional.png

Test sequence_lollipop_groups_by-meth_condensed.png

Test sequence_lollipop_groups_by-meth_proportional.png

Test sequence_lollipop_groups_clust_condensed.png

Test sequence_lollipop_groups_clust_proportional.png

Test sequence_lollipop_replicates_as-is_condensed.png

Test sequence_lollipop_replicates_as-is_proportional.png

Test sequence_lollipop_replicates_by-group_condensed.png

Test sequence_lollipop_replicates_by-group_proportional.png

Test sequence_lollipop_replicates_by-meth_condensed.png

Test sequence_lollipop_replicates_by-meth_proportional.png

Test sequence_lollipop_replicates_clust_condensed.png

Test sequence_lollipop_replicates_clust_proportional.png

meth_profile_plots

Test sequence_meth_profile_collection1_condensed_psign.png

Test sequence_meth_profile_collection1_condensed_pval.png

Test sequence_meth_profile_collection1_proportional_psign.png

Test sequence_meth_profile_collection1_proportional_pval.png

Test sequence_meth_profile_collection2_condensed_psign.png

Test sequence_meth_profile_collection2_condensed_pval.png

Test sequence_meth_profile_collection2_proportional_psign.png

Test sequence_meth_profile_collection2_proportional_pval.png

tables

Test sequence_descriptive_statistics_means.csv

Test sequence_descriptive_statistics_means.xlsx

Test sequence_descriptive_statistics_positions.csv

Test sequence_descriptive_statistics_positions.xlsx

Test sequence_methylation_table_groups.csv

Test sequence_methylation_table_groups.xlsx

Test sequence_methylation_table_replicates.csv

Test sequence_methylation_table_replicates.xlsx

Test sequence_t_test_table_means.csv

Test sequence_t_test_table_means.xlsx

Test sequence_t_test_table_positions.csv

Test sequence_t_test_table_positions.xlsx